Differences

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--- kraken-software [2022/07/07 11:27] – aorth
+++ kraken-software [2023/08/11 10:13] (current) – aorth
@@ Line 31: / Line 31: @@
 $ sudo chown root /export/apps/kraken/2.1.2/*</code>
-Download some [[ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/|pre-formatted databases]] and extract them somewhere:
+Download some [[https://benlangmead.github.io/aws-indexes/k2|pre-formatted databases]] and extract them somewhere:
-<code>$ sudo mkdir -p /export/data/bio/kraken2/db
+<code>$ cd /var/scratch
-$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/16S_Greengenes_20190418.tgz
+$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Greengenes13.5_20200326.tgz
-$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v1_8GB_201904_UPDATE.tgz
+$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva132_20200326.tgz
-$ wget ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_v2_8GB_201904_UPDATE.tgz
+$ wget https://genome-idx.s3.amazonaws.com/kraken/16S_Silva138_20200326.tgz
 $ for name in *.tgz; do sudo tar xfv "$name" -C /export/data/bio/kraken2/db; done</code>
-Download the larger standard pre-formatted database:
+Download several larger databases (careful about space!):
-<code>$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20210517.tar.gz
+<code>$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_standard_20230605.tar.gz
-$ tar xf k2_standard_20210517.tar.gz
+$ wget https://genome-idx.s3.amazonaws.com/kraken/k2_nt_20230502.tar.gz</code>
-$ sudo mkdir -p /export/data/bio/kraken2/db/standard
-$ sudo cp database* hash.k2d inspect.txt opts.k2d seqid2taxid.map taxo.k2d /export/data/bio/kraken2/db/standard</code>
 The ''kraken2'' application finds these with the ''KRAKEN2_DB_PATH'' environment variable.